This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Understanding the molecular structure and dynamics of condensed phases is a major goal of chemists. Infrared (IR) spectroscopy is a powerful technique used to study the structures of substances via analysis of characteristic absorption bands. Recent advances in laser techniques and ultrafast nonlinear IR spectroscopy enable researchers to obtain valuable structural and dynamic information on systems in the condensed phase. One of our research groups focuses is the theory and simulation of condensed phase spectroscopy. Previous work utilizing the facility at SDSC has allowed us to modify the GROMACS code to output frequency trajectories on-the-fly for the amide-I spectra calculation of a tetrameric peptide bundle, CD3-zeta. We are extending the method we have developed to investigate the spectral signature accompanying the amyloid aggregation. Large and fast computational environments provided by the TeraGrid sites will facilitate the computation and understanding of FT-IR and 2D-IR spectra of amyloid monomer/aggregates. In addition, we are currently developing an output data manipulation for instantaneous lineshape calculation and extending our methodology to coupled-chromophore systems.